Extended Data Fig. 6: Simulations to understand our definitions of “shared” and “GxE” SNPs.
From: Dietary stress remodels the genetic architecture of lifespan variation in outbred Drosophila
We classify SNPs as having “shared” effect sizes between environments (defined as FDR < 10% in one environment and p < 0.05 in the other) or “GxE” effects where the lifespan effect is stronger on one diet relative to the other (“GxE” defined as FDR < 10% in one environment and p < 0.05 in the other). To understand how this thresholding affected our results, we simulated 121 datasets of 1000 loci each where the lifespan reducing allele decreased by 0-20% with identical or varied effect sizes across two environments (sample sizes = 1000 individuals at T0 and 1000 at each of the two TN end points). For each simulation, we recorded the number of loci that would be classified as (A) shared (p < 10−4.5 in one environment, similar to a 10% FDR in our real dataset, and p < 0.05 in the other environment) or (B) GxE (p < 10−4.5 in environment #2 and p > 0.05 in environment #1). See Text S6 for additional details. (C) The FDR cutoff used to define GxE effects (that is, the threshold used to consider a site significant in one environment) versus the false positive rate estimated from permutations where the TN HS and TN CTRL labels were scrambled 10 times. See Text S6 for additional details.
